Simulation of multiple RNA-seq experiments

Description

Usage

Arguments

param

Mean expression levels: param must be a data frame containing at least two columns named
"mucond1" and "mucond2" and one row per gene.

dispFuncs

List of length equal to the number of studies to be simulated, containing the gamma regression parameters
describing the mean-dispersion relationship for each one; these are the mean-dispersion functions linking mean
and intra-study variability for each independent experiment.

nrep

Number of replicates to be simulated in each condition in each study. Ignored if classes is filled.

classes

List of class memberships, one per study (maximum 20 studies). Each vector or factor of the list can only
contain two levels which correspond to the two conditions studied. If NULL, classes is built as a
list of two vectors with nrep labels 1 (for condition 1) and nrep labels 2 (for condition 2).

inter.sd

Inter-study variability. By default, inter.sd is set to 0.3, which corresponds to a moderate inter-study
variability in the case where param and dispFuncs parameters are used to simulate data.

Details

Details about the simulation procedure are given in the following paper:

Value

A matrix with simulated expression levels, one row per gene and one column per replicate. Names of studies are given
in the column names of the matrix.

Note

If the param data provided in this package are not used to simulate data, one should check that the
per-condition means in param are reasonable. Note also that for genes to be simulated as non-differentially
expressed, the values of "mucond1" and "mucond2" in param should be equal.